NucPred on Proteomes

Authors: Andrea Krings, Amine Heddad, Markus Brameier and Bob MacCallum, Stockholm Bioinformatics Center, Stockholm University, Sweden.

NucPred - predictions for eukaryotic proteomes

Species:

Note: All filters/tests are combined with AND unless otherwise stated

Show only the proteins with links to database(s):
OMIM - human disease genes
PDB - protein 3D structure
( AND OR combination )

Annotation filters (can be slow! - Perl regexps allowed: e.g. nucleus|nucleolus)

UniProt ID (e.g. "PK3B_")
UniProt description (e.g. "kinase")
UniProt subcellular location
AND
UniProt GO component
AND
AND the
AND the

Only show proteins where the PredictNLS prediction is:

positive
negative

Only show proteins where the PSORT II predicted location

is is not

Click here: to filter by NucPred score

exclude all transmembrane proteins predicted by TMHMM
don't exclude lone N-terminal predicted transmembrane helices
(these could be signal peptides)

export all ACs and IDs as text file

Show proteins (ordered by NucPred score ) from to (currently 98716 matches)

You can bookmark/save your search criteria with this link. You can also start again with default settings.

UniProt accession	UniProt ID	UniProt description	NucPred score	Predict- NLS	PSORT II	TMHMM #helices	UniProt annotation for subcellular location	Uniprot GO cellular component	OMIM	PDB	sequence length
O00587 UniProt NPD GO	MFNG_HUMAN	Beta-1,3-N-acetylglucosaminyltransferase manic fringe (EC 2.4.1.222) (O-fucosylpeptide 3-beta-N-acet ...	0.38	-	exc	0	Golgi apparatus; Golgi membrane; single-pass type II membrane protein (By similarity)	extracellular space [TAS]	602577		321
Q9YHB3 UniProt NPD GO	RFNG_NOTVI	Beta-1,3-N-acetylglucosaminyltransferase radical fringe (EC 2.4.1.222) (nrFng) (O-fucosylpeptide 3-b ...	0.38	-	mit	1 *	Golgi apparatus; Golgi membrane; single-pass type II membrane protein (Potential)				396
P83961 UniProt NPD GO	BNCB_BENHI	Beta-benincasin (Fragment)	0.38	-		0					14
Q02248 UniProt NPD GO	CTNB1_MOUSE	Beta-catenin	0.38	-	cyt	0	Cytoplasm. Cytoplasmic when it is unstabilized (high level of phosphorylation) or bound to CDH1. Nuc ...	apical part of cell [IDA] basolateral plasma membrane [IDA] cell-cell adherens junction [IDA] cytoplasm [IDA] lamellipodium [IDA] lateral plasma membrane [IDA] membrane fraction [IDA] nucleus [IDA] plasma membrane [IDA] transcription factor complex [IDA]		3BCT	781
Q95104 UniProt NPD GO	PDYN_BOVIN	Beta-neoendorphin-dynorphin precursor (Proenkephalin B) (Preprodynorphin) [Contains: Beta-neoendorph ...	0.38	-	exc	0	Secreted protein				258
P01061 UniProt NPD GO	IBB2_PHAAN	Bowman-Birk type proteinase inhibitors I-A, I-B, and I-A'	0.38	-	nuc	0					78
Q61361 UniProt NPD GO	PGCB_MOUSE	Brevican core protein precursor	0.38	-	exc	0	Secreted protein; extracellular space; extracellular matrix (By similarity)				883
Q9BZH6 UniProt NPD GO	BRWD2_HUMAN	Bromodomain and WD repeat domain-containing protein 2 (WD repeat protein 11)	0.38	-	nuc	0			606417		1224
O75596 UniProt NPD GO	CLC3A_HUMAN	C-type lectin domain family 3 member A precursor (C-type lectin superfamily member 1) (Cartilage-der ...	0.38	-	mit	0					197
P28033 UniProt NPD GO	CEBPB_MOUSE	CCAAT/enhancer-binding protein beta (C/EBP beta) (Interleukin-6-dependent-binding protein) (IL-6DBP) ...	0.38	+	nuc	0	Nucleus	cytoplasm [IDA] nucleus [IDA]		1CI6	296
Q3T0B9 UniProt NPD GO	CEBPG_BOVIN	CCAAT/enhancer-binding protein gamma (C/EBP gamma)	0.38	+	nuc	0	Nucleus (By similarity)				149
P26801 UniProt NPD GO	CEBPG_RAT	CCAAT/enhancer-binding protein gamma (C/EBP gamma)	0.38	+	nuc	0	Nucleus	nucleus [ISS]			150
P38337 UniProt NPD GO	SHG1_YEAST	COMPASS component SHG1 (Complex proteins associated with SET1 protein SHG1) (Set1C component SHG1)	0.38	-	nuc	0	Nucleus (Probable)	COMPASS complex [IPI] nucleus [IDA]			142
Q8LAZ7 UniProt NPD GO	CSN5B_ARATH	COP9 signalosome complex subunit 5b (EC 3.4.-.-) (Signalosome subunit 5b) (Jun activation domain-bin ...	0.38	-	nuc	0	Cytoplasm. Nucleus				357
Q9H9Q2 UniProt NPD GO	CSN7B_HUMAN	COP9 signalosome complex subunit 7b (Signalosome subunit 7b) (SGN7b) (JAB1-containing signalosome su ...	0.38	-	nuc	0	Cytoplasm. Nucleus				264
Q8BV13 UniProt NPD GO	CSN7B_MOUSE	COP9 signalosome complex subunit 7b (Signalosome subunit 7b) (SGN7b) (JAB1-containing signalosome su ...	0.38	-	nuc	0	Cytoplasm (By similarity). Nucleus (By similarity)				264
Q9WVR7 UniProt NPD GO	PPM1F_RAT	Ca(2+)/calmodulin-dependent protein kinase phosphatase (EC 3.1.3.16) (CaM-kinase phosphatase) (CaMKP ...	0.38	-	cyt	0					450
P19534 UniProt NPD GO	CADH2_BOVIN	Cadherin-2 precursor (Neural-cadherin) (N-cadherin) (CDw325 antigen) (Fragment)	0.38	-	nuc	1	Membrane; single-pass type I membrane protein				877
P59862 UniProt NPD GO	CAD26_MOUSE	Cadherin-like protein 26 precursor	0.38	-	end	1	Membrane; single-pass type I membrane protein (By similarity)				763
Q95V25 UniProt NPD GO	SLO1_CAEEL	Calcium-activated potassium channel slo-1 (Maxi K channel) (MaxiK) (BK channel) (Slo homolog) (Slowp ...	0.38	-	end	7 *	Membrane; multi-pass membrane protein (Probable)				1140
O88751 UniProt NPD GO	CABP1_RAT	Calcium-binding protein 1 (CaBP1) (Caldendrin)	0.38	-	nuc	0	Occurs in both the cytoplasmic and cytoskeletal compartment of cell somata and dendrites	cytoskeleton [IDA] dendrite [IDA]			298
P38929 UniProt NPD GO	ATC2_YEAST	Calcium-transporting ATPase 2 (EC 3.6.3.8) (Vacuolar Ca(2+)-ATPase)	0.38	-	end	9	Vacuole; vacuolar membrane; multi-pass membrane protein	vacuolar membrane (sensu Fungi) [IDA]			1173
P54750 UniProt NPD GO	PDE1A_HUMAN	Calcium/calmodulin-dependent 3',5'-cyclic nucleotide phosphodiesterase 1A (EC 3.1.4.17) (Cam-PDE 1A) ...	0.38	-	cyt	0			171890	1LXQ	534
Q00168 UniProt NPD GO	KCC2A_DROME	Calcium/calmodulin-dependent protein kinase type II alpha chain (EC 2.7.11.17) (CaM-kinase II alpha ...	0.38	-	cyt	0		calcium- and calmodulin-dependent protein k... [TAS]			530
Q9GKR6 UniProt NPD GO	CAYP2_MACFA	Calcyphosin-2 (Calcyphosine-2)	0.38	-	cyt	0					313
Q38798 UniProt NPD GO	CALX2_ARATH	Calnexin homolog 2 precursor	0.38	-	end	2 *	Endoplasmic reticulum; endoplasmic reticulum membrane; single-pass type I membrane protein (By simil ...				532
P06815 UniProt NPD GO	CAN1_RABIT	Calpain-1 catalytic subunit (EC 3.4.22.52) (Calpain-1 large subunit) (Calcium-activated neutral prot ...	0.38	-	cyt	0	Cytoplasm (By similarity). Cell membrane (By similarity). Translocates to the plasma membrane upon C ...				302
Q95LP4 UniProt NPD GO	CAN10_MACFA	Calpain-10 (EC 3.4.22.-) (Calcium-activated neutral proteinase 10) (CANP 10)	0.38	-	cyt	0					653
Q5AK25 UniProt NPD GO	PALB_CANAL	Calpain-like protease palB/RIM13 (EC 3.4.22.-) (Cysteine protease RIM13)	0.38	-	nuc	0					717
P48284 UniProt NPD GO	CAH4_RAT	Carbonic anhydrase 4 precursor (EC 4.2.1.1) (Carbonic anhydrase IV) (Carbonate dehydratase IV) (CA-I ...	0.38	-	exc	0	Cell membrane; lipid-anchor; GPI-anchor (By similarity)				309
P22792 UniProt NPD GO	CPN2_HUMAN	Carboxypeptidase N subunit 2 precursor (Carboxypeptidase N polypeptide 2) (Carboxypeptidase N 83 kDa ...	0.38	-	nuc	0	Secreted protein	extracellular region [NAS]	603104		545
P06731 UniProt NPD GO	CEAM5_HUMAN	Carcinoembryonic antigen-related cell adhesion molecule 5 precursor (Carcinoembryonic antigen) (CEA) ...	0.38	-	nuc	0	Cell membrane; lipid-anchor; GPI-anchor	integral to plasma membrane [TAS]	114890	1E07	702
Q8IUL8 UniProt NPD GO	CILP2_HUMAN	Cartilage intermediate layer protein 2 precursor (CILP-2) [Contains: Cartilage intermediate layer pr ...	0.38	-	vac	0	Secreted protein; extracellular space; extracellular matrix (By similarity)				1156
P67962 UniProt NPD GO	KC1A_CHICK	Casein kinase I isoform alpha (EC 2.7.11.1) (CKI-alpha) (CK1)	0.38	-	cyt	0	Cytoplasm (By similarity)				337
P48729 UniProt NPD GO	KC1A_HUMAN	Casein kinase I isoform alpha (EC 2.7.11.1) (CKI-alpha) (CK1)	0.38	-	cyt	0	Cytoplasm		600505		337
Q8BK63 UniProt NPD GO	KC1A_MOUSE	Casein kinase I isoform alpha (EC 2.7.11.1) (CKI-alpha) (CK1)	0.38	-	cyt	0	Cytoplasm (By similarity)				337
P67963 UniProt NPD GO	KC1A_XENLA	Casein kinase I isoform alpha (EC 2.7.11.1) (CKI-alpha) (CK1)	0.38	-	cyt	0	Cytoplasm (By similarity)				337
P68399 UniProt NPD GO	CSK21_BOVIN	Casein kinase II subunit alpha (EC 2.7.11.1) (CK II)	0.38	-	mit	0					391
P68400 UniProt NPD GO	CSK21_HUMAN	Casein kinase II subunit alpha (EC 2.7.11.1) (CK II)	0.38	-	mit	0			115440	1YMI	391
Q60737 UniProt NPD GO	CSK21_MOUSE	Casein kinase II subunit alpha (EC 2.7.11.1) (CK II)	0.38	-	mit	0		protein kinase CK2 complex [TAS]			391
Q99638 UniProt NPD GO	RAD9A_HUMAN	Cell cycle checkpoint control protein RAD9A (EC 3.1.11.2) (DNA repair exonuclease rad9 homolog A) (h ...	0.38	-	nuc	0	Nucleus	nucleus [TAS]	603761		391
Q6AY41 UniProt NPD GO	CC50A_RAT	Cell cycle control protein 50A (Transmembrane protein 30A)	0.38	-	mit	2 *	Membrane; multi-pass membrane protein (Potential)				328
Q8LPK5 UniProt NPD GO	CESA8_ARATH	Cellulose synthase A catalytic subunit 8 [UDP-forming] (EC 2.4.1.12) (AtCesA-8) (Irregular xylem pro ...	0.38	-	end	8	Cell membrane; multi-pass membrane protein (Probable)				985
Q8R2V5 UniProt NPD GO	CENA2_MOUSE	Centaurin-alpha 2	0.38	-	cyt	0	Cytoplasm (By similarity). Cell membrane (By similarity). Constitutively associated with the plasma ...	cytoplasm [ISS] mitochondrial envelope [ISS] plasma membrane [ISS]			381
Q5RCP7 UniProt NPD GO	CEP76_PONPY	Centrosomal protein of 76 kDa (Cep76 protein)	0.38	-	nuc	0	Centrosome (By similarity)				658
Q4QQV8 UniProt NPD GO	CHMP5_RAT	Charged multivesicular body protein 5 (Chromatin-modifying protein 5)	0.38	-	nuc	0	Cytoplasm; cytosol (By similarity)				219
Q9D7S9 UniProt NPD GO	CHMP5_MOUSE	Charged multivesicular body protein 5 (Chromatin-modifying protein 5) (SNF7 domain-containing protei ...	0.38	-	nuc	0	Cytoplasm; cytosol (By similarity)	nucleus [IDA]			219
Q08054 UniProt NPD GO	CSI2_YEAST	Chitin synthase 3 complex protein CSI2	0.38	-	end	1		bud neck [IDA] vacuole (sensu Fungi) [IDA]			341
Q8MX31 UniProt NPD GO	IDGF3_DROYA	Chitinase-like protein Idgf3 precursor (Imaginal disk growth factor protein 3)	0.38	-	cyt	0	Secreted protein (By similarity). Secreted in hemolymph (By similarity). It is probably transported ...	extracellular region [ISS]			441
P51797 UniProt NPD GO	CLCN6_HUMAN	Chloride channel protein 6 (ClC-6)	0.38	-	end	9	Membrane; multi-pass membrane protein	integral to membrane [NAS]	602726		869

You are viewing entries 33251 to 33300 of 98716. You can see more proteins by changing the limits in the form at the top of this page, or click here for the next page of proteins .

If you find NucPred useful, please cite this paper:

NucPred - Predicting Nuclear Localization of Proteins. Brameier M, Krings A, Maccallum RM. Bioinformatics, 2007. PubMed id: 17332022

The authors also look forward to your comments and suggestions.

What does the NucPred score mean?

You have to decide on a NucPred score threshold. Sequences which score greater than or equal to this threshold are predicted to spend some time in the nucleus. Higher thresholds yield fewer predicted nuclear proteins, but these predictions are more accurate (you can have higher confidence in them). The table below gives more details of the performance of NucPred estimated using the sequences it was trained on (by cross-validation). Another benchmark is available in the Bioinformatics 2007 paper.

NucPred score threshold	Specificity	Sensitivity
see above	fraction of proteins predicted to be nuclear that actually are nuclear	fraction of true nuclear proteins that are predicted (coverage)
0.10	0.45	0.88
0.20	0.52	0.83
0.30	0.57	0.77
0.40	0.63	0.69
0.50	0.70	0.62
0.60	0.71	0.53
0.70	0.81	0.44
0.80	0.84	0.32
0.90	0.88	0.21
1.00	1.00	0.02

Sequences which score >= 0.8 with NucPred and which are predicted by PredictNLS to contain an NLS have been shown to be 93% correct with a coverage of 16%. (PredictNLS by itself is 87% correct with 26% coverage on the same data.)

Go back to the NucPred Home Page.